Benchling supports four different methods of importing DNA. They all begin by clicking the Create (or +) button on the left side panel.

After clicking Create, hover over DNA Sequence and then click New DNA Sequence. 

You’ll have four options to import a DNA sequence into Benchling and save it to any project or folder.

Import from your computer

Click here to download pBR322 to your computer to practice importing a file into Benchling.

  1. Select the folder and project on Benchling where you would like your sequence to be saved.

  2. Drag and drop a file or click the Choose a File button to locate the file on your computer. We also support importing zip files or selecting multiple files at once to import multiple sequences simultaneously.

  3. Use the menu that appears to adjust sequence properties.

After uploading your file, use the menu that appears to change the file location, sequence topology, or tags associated with the file.

Import from a database

Benchling let’s you import DNA sequences from external databases by simply typing in the name of the gene.

You can even specify different ID’s depending on the place you want to import the sequence from. We support the following inputs for pulling DNA from external databases:

  • NCBI Accession Number 

  • Addgene URL 

  • Ensembl ID 

  • iGEM Registry 

  • BioBrick ID 

  • Joint BioEnergy Institute (JBEI) ID 

Import from a genomic locus

Benchling supports many preloaded genomes. Import DNA from any of these genomes by specifying the locus. You’ll be able to choose the chromosome and exactly which base pairs to pull from the genome.

Input a raw sequence

Directly input a sequence into Benchling. You can paste a sequence directly from your computer’s clipboard into the window or type it out manually. Specify the topology of your sequence as linear or circular.

What sequence file formats does Benchling support?

Benchling supports a wide range of file formats, including both common and proprietary ones. We’re constantly updating the formats we support, so just try dragging in your files into the importer – our goal is to have the importer “just work” regardless of the file format.

The most common two file formats are GenBank and FASTA. Benchling fully supports these two formats, so when encountering importer errors or trying to import sequences from an unsupported format, a quick workaround is to “save as” to either format as most applications can export either Genbank or FASTA.

The following formats are fully supported in Benchling – the sequence, annotations, and comments will all be directly imported into Benchling. To avoid import errors, please ensure your file names are written as shown in the table below. For example, if you are importing a file named "FILE" with multiple sequences using FASTA, the file name should be “FILE.fasta” so Benchling can recognize the file and upload multiple sequences separately.

Unsupported File Types

At the moment, Benchling unfortunately cannot parse out sequences saved as PDF or as Microsoft Word files (doc, docx). The easiest way to get these sequences into Benchling is to create a new sequence and then copy and paste in the bases.

Footnotes

  1. The file extension of the format. Benchling sometimes tries to guess the file format by extension, so if you ever encounter importer errors and the file extension doesn’t match the table, try renaming the file and then reimporting.

  2. Files in this column are archives that can potentially contain more than one sequence. When a multi-sequence file is imported, Benchling will automatically split the archive and import each individual sequence into your library. (Most other applications will ignore all sequences past the first, so the behavior may differ slightly).

  3. Files in this column are results from Sanger sequencing, and will contain chromatogram traces along with quality data when imported as an alignment.

What's next?

After reviewing this tutorial you can next learn how to view and change display features on your sequences.

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